idea
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===== Interactive Display for Evolutionary Analyses ===== | ===== Interactive Display for Evolutionary Analyses ===== | ||
- | The installer | + | IDEA (Interactive Display for Evolutionary Analyses) |
http:// | http:// | ||
+ | |||
+ | ===== Installation ===== | ||
+ | |||
+ | These notes were made when the HPC was running Rocks 4.1, so they may or may not work the same way after the cluster is upgraded to Rocks 5.2. You may find want to make sure the pre-requisites are installed before going on. The IDEA website has documentation but the installation literature is VERY limited! | ||
+ | |||
+ | <note warning> | ||
+ | |||
+ | Unpack the archive into a new folder: | ||
+ | * < | ||
+ | $ cd idea | ||
+ | $ tar zxf ../ | ||
+ | $ ls | ||
+ | apache-batik | ||
+ | CheckAvailableMemory.class | ||
+ | CheckAvailableMemory.java | ||
+ | check-java-memory | ||
+ | commons-io | ||
+ | DEFAULT-BASEML.ctl | ||
+ | DEFAULT-CODEML.ctl | ||
+ | delete-old-event-logs | ||
+ | Run the installer: | ||
+ | * < | ||
+ | Checking for required Perl modules... | ||
+ | Unpacking wf-3.1.1.tar.gz... | ||
+ | Using grid type sge! | ||
+ | Configuring Workflow... | ||
+ | Unpacking jruby-bin-1.0.0RC1.tar.gz... | ||
+ | Checking for required PHYLIP programs... | ||
+ | Checking for required PAML programs... | ||
+ | Checking for other required programs... | ||
+ | Unpacking PDFBox-0.7.2.zip... | ||
+ | Unpacking jdic-20060613-bin-cross-platform.zip... | ||
+ | Unpacking xstream-distribution-1.2.1-src.zip... | ||
+ | Configuring IDEA... | ||
+ | Compiling... | ||
+ | Congratulations! | ||
+ | You may find it convenient to add / | ||
+ | |||
+ | SGE event logs will be stored in / | ||
+ | This directory should be cleaned out periodically. | ||
+ | The script delete-old-event-logs may be used for this purpose. | ||
+ | |||
+ | NOTICE TO SGE (SUN GRID ENGINE) USERS: | ||
+ | ====================================== | ||
+ | IDEA uses the Workflow process management system to manage grid submissions. | ||
+ | In order to work with SGE, Workflow requires the following set-up by a grid administrator: | ||
+ | The scripts / | ||
+ | |||
+ | Grid submissions have been temporarily disabled. | ||
+ | You may still use IDEA, but all processes will be executed on the machine from which you launch IDEA. | ||
+ | |||
+ | Once an administrator has installed these scripts, rename / | ||
+ | |||
+ | (If Workflow has already been installed on your grid, prolog and epilog do not need to be reinstalled.)</ | ||
+ | The program has a funny installer, as the software package isn't really " | ||
+ | |||
+ | Replace all instances of " | ||
+ | * < | ||
+ | Copy the directory to somewhere more appropriate (using '' | ||
+ | * < | ||
+ | $ sudo cp -R idea / | ||
+ | Change everything to 777 permissions, | ||
+ | < | ||
+ | Add the installed directory to your shell' | ||
+ | * < |
idea.1250603226.txt.gz · Last modified: 2010/05/22 14:19 (external edit)